Table 3.
Identified binding cavities in Ns/Ka/Cs H-NOX systems. Occupancy by at least one ligand molecule over the trajectory is given in %. In the case of the NO-containing systems, the average number and the observed maximum number of NO molecules in the pockets are also shown. For the distal pockets further information is given. The spatial distribution of the pockets is depicted in Figure 5.
| Binding Pockets | NO | O2 | CO |
|---|---|---|---|
| Cs H-NOX | |||
| Distal pocket: | 99.3%/1.32/4 | 92.8% | 91.13% |
| average distance of centroid of gas molecule—FE | 4.0 Å | 3.95 Å | 4.3 Å |
| average length of being trapped | 920.2 ps | 189.8 ps | 609.0 ps |
| number of in-and-out event | 323 | 1469 | 463 |
| Proximal pocket: | 47.90%/1.09/2 | 28.6% | 0.0% |
| Tunnel 1 (Xe2 and Xe3): | |||
| Xe2: | 89.6%/1.08/4 | 50.7% | 65.2% |
| Xe3: | 92.4%/1.21/4 | 57.5% | 56.1% |
| Tunnel 2 (Side-propionate): | 96.0%/1.51/4 | 40.4% | 24.0% |
| Tunnel 3 (Side-entrance): | 27.8%/1.08/3 | 18.0% | 16.6% |
| Surface pockets (SP): | |||
| Distal surface pocket (DSP): | 75.8%/1.00/1 | 38.3% | 34.2% |
| Proximal surface pocket 1 (P1SP) (αF, αE): | 66.8%/1.02/2 | 55.7% | 45.4% |
| Proximal surface pocket 2 (P2SP) (αF, β-sheet): | 99.25%/1.00/2 | 9.0% | 12.8% |
| Ka H-NOX | |||
| Distal pocket: | 86.1%/1.32/4 | 42.2% | 13.5% |
| average distance of centroid of gas molecule—FE | 5.3 Å | 5.1 Å | 5.6 Å |
| average length of being trapped | 116.0 ps | 59.0 ps | 45.0 ps |
| number of transfer events in-and-out | 2258 | 2255 | 922 |
| Proximal: | 99.95%/1.00/2 | 75.1% | 99.44% |
| Tunnel 1 (Xe2 and Xe3): | |||
| XE2: | 87.64%/1.10/4 | 26.4% | 55.65% |
| XE3: | 95.6%/1.11/3 | 37.9% | 76.3% |
| Tunnel 2 (Side-propionate): | 29.2%/1.04/3 | 10.7% | 16.67% |
| Tunnel 3 (Side-entrance): | 86.6%/1.20/4 | 18.2% | 22.0% |
| Buried pockets/cavities (BP):BP1: | 94.8%/1.21/3 | 21.3% | 13.4% |
| Cs H-NOX | |||
| Distal pocket: | 64.8%/1.2/2 | 44.4% | 0.0% |
| average distance of centroid of gas molecule—FE | 4.3 Å | 3.6 Å | - |
| average length of being trapped in distal pocket | 27.5 ps | 86.6 ps | - |
| Proximal pocket: | 3.3%/1.00/1 | 56.9% | 0.4% |
| Accessible-binding sites in the diffusion tunnels: | 82.7%/1.00/2 | 22.2% | 75.1% |
| Tunnel 2 (Side-propionate): | |||
| Proximal surface pocket 1 (P1SP) (αF, αE): | 10.2%/1.01/2 | 12.8% | 84.4% |
| Buried pockets/cavities (BP): | |||
| BP1: | 0.2%/1.00/1 | 69.5% | 0.0% |
| BP2: | 5.8%/1.00/2 | 28.5% | 99.3% |
| BP3: | 39.5%/1.00/1 | 4.0% | 0.0% |